Mark Gerstein

Selected Publications:

• JC Mu, M Mohiyuddin, J Li, NB Asadi, MB Gerstein, A Abyzov, WH Wong, HY Lam (2014). "VarSim: A high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications." Bioinformatics. 
• RR Kitchen, JS Rozowsky, MB Gerstein, AC Nairn (2014). "Decoding neuroproteomics: integrating the genome, translatome and functional anatomy." Nat Neurosci 17: 1491-9. [PMID: 25349915]
  A Harmanci, J Rozowsky, M Gerstein (2014). "MUSIC: Identification of Enriched Regions in ChIP-Seq Experiments using a Mappability-Corrected Multiscale Signal Processing Framework." Genome Biol 15: 474. 
• Y Fu, Z Liu, S Lou, J Bedford, X Mu, KY Yip, E Khurana, M Gerstein (2014). "FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer." Genome Biol 15: 480. 
• AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, LW Hillier, J Janette, L Jiang, D Kasper, T Kawli, P Kheradpour, A Kundaje, JJ Li, L Ma, W Niu, EJ Rehm, J Rozowsky, M Slattery, R Spokony, R Terrell, D Vafeados, D Wang, P Weisdepp, YC Wu, D Xie, KK Yan, EA Feingold, PJ Good, MJ Pazin, H Huang, PJ Bickel, SE Brenner, V Reinke, RH Waterston, M Gerstein, KP White, M Kellis, M Snyder (2014). "Comparative analysis of regulatory information and circuits across distant species." Nature 512: 453-6. 
• MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, CA Davis, L Hillier, C Sisu, JJ Li, B Pei, AO Harmanci, MO Duff, S Djebali, RP Alexander, BH Alver, R Auerbach, K Bell, PJ Bickel, ME Boeck, NP Boley, BW Booth, L Cherbas, P Cherbas, C Di, A Dobin, J Drenkow, B Ewing, G Fang, M Fastuca, EA Feingold, A Frankish, G Gao, PJ Good, R Guigó, A Hammonds, J Harrow, RA Hoskins, C Howald, L Hu, H Huang, TJ Hubbard, C Huynh, S Jha, D Kasper, M Kato, TC Kaufman, RR Kitchen, E Ladewig, J Lagarde, E Lai, J Leng, Z Lu, M MacCoss, G May, R McWhirter, G Merrihew, DM Miller, A Mortazavi, R Murad, B Oliver, S Olson, PJ Park, MJ Pazin, N Perrimon, D Pervouchine, V Reinke, A Reymond, G Robinson, A Samsonova, GI Saunders, F Schlesinger, A Sethi, FJ Slack, WC Spencer, MH Stoiber, P Strasbourger, A Tanzer, OA Thompson, KH Wan, G Wang, H Wang, KL Watkins, J Wen, K Wen, C Xue, L Yang, K Yip, C Zaleski, Y Zhang, H Zheng, SE Brenner, BR Graveley, SE Celniker, TR Gingeras, R Waterston (2014). "Comparative analysis of the transcriptome across distant species." Nature 512: 445-8. 
• C Sisu, B Pei, J Leng, A Frankish, Y Zhang, S Balasubramanian, R Harte, D Wang, M Rutenberg-Schoenberg, W Clark, M Diekhans, J Rozowsky, T Hubbard, J Harrow, MB Gerstein (2014). "Comparative analysis of pseudogenes across three phyla." Proc Natl Acad Sci U S A 111: 13361-6.